De novo genome assembly depicts the immune genomic characteristics of cattle

Li, Ting-Ting; Xia, Tian; Wu, Jia-Qi; Hong, Hao; Sun, Zhao-Lin; Wang, Ming; Ding, Fang-Rong; Wang, Jing; Jiang, Shuai; Li, Jin; Pan, Jie; Yang, Guang; Feng, Jian-Nan; Dai, Yun-Ping; Zhang, Xue-Min; Zhou, Tao; Li, Tao

doi:10.1038/s41467-023-42161-1

Cited by 5 publications

(4 citation statements)

References 66 publications

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“…To date, T2T-goat1.0 is one of several complete seamless mammal genomes, similar to those of human 10,11 , gerbil 44 and cattle 45 . With the advancement of T2T-goat1.0 , a black box corresponding to highly repetitive regions was uncovered, especially for centromeric regions.…”

Section: Discussionmentioning

confidence: 99%

Telomere-to-telomere genome assembly of a male goat reveals novel variants associated with cashmere traits

Wu,

Luo,

Zhang

et al. 2024

Preprint

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A complete goat (Capra hircus) reference genome enhances analyses of genetic variation, thus providing novel insights into domestication and selection in goats and related species. Here, we assembled a telomere-to-telomere (T2T) gap-free genome (2.86 Gb) from a cashmere goat (T2T-goat1.0), which included a Y chromosome of 20.9 Mb. With a base accuracy of >99.999%, T2T-goat1.0 corrected numerous genome-wide structural and base errors in previous assemblies and added 288.5 Mb of previously unresolved regions (PURs) and 446 newly assembled genes to the reference genome. We sequenced the genomes of five representative goat breeds for PacBio reads, and used T2T-goat1.0 as a reference to identify a total of 63,417 structural variations (SVs) with up to 4711 SVs (7.41%) in the PURs and 507 overlapping genes significantly enriched (Padj. < 0.05) in the keratin filament pathway. T2T-goat1.0 was applied in population analyses of global wild and domestic goats, which revealed 32,419 SVs and 25,397,794 SNPs, including 870 SVs and 545,026 SNPs in the PURs. Also, our analyses revealed a set of novel selective variants and genes associated with domestication (e.g., NKG2D and ABCC4) and cashmere traits (e.g., ABCC4 and ASIP).

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Section: Discussionmentioning

confidence: 99%

Telomere-to-telomere genome assembly of a male goat reveals novel variants associated with cashmere traits

Wu,

Luo,

Zhang

et al. 2024

Preprint

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“…Since the release of human T2T-CHM13, T2T genome assemblies have become popular and available for several species 16,44,45 . Nevertheless, several gaps are still present in recent nearly complete animal genome assemblies, including those of chicken 46 , duck 47 , Mongolian gerbil 48 , and cattle 49 . The T2T-sheep1.0 genome assembled here represents the first gap-free T2T genome of a ruminant, which we obtained by resolving PURs, particularly those in centromeres and on the Y chromosome (T2T-sheep-chrY).…”

Section: Discussionmentioning

confidence: 99%

Telomere-to-telomere sheep genome assembly reveals new variants associated with wool fineness trait

Luo,

Wu,

Zhao

et al. 2024

Preprint

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Ongoing efforts to improve sheep reference genome assemblies still leave many gaps and incomplete regions, resulting in a few common failures and errors in sheep genomic studies. Here, we report a complete, gap-free telomere-to-telomere (T2T) genome of a ram (T2T-sheep1.0) with a size of 2.85 Gb, including all autosomes and chromosomes X and Y. It adds 220.05 Mb of previously unresolved regions (PURs) and 754 new genes to the most updated reference assembly, ARS-UI_Ramb_v3.0, and contains four types of repeat units (SatI, SatII, SatIII, and CenY) in the centromeric regions. T2T-sheep1.0 exhibits a base accuracy of >99.999%, corrects several structural errors in previous reference assemblies, and improves structural variant (SV) detection in repetitive sequences. We identified 192,265 SVs, including 16,885 new SVs in the PURs, from the PacBio long-read sequences of 18 global representative sheep. With the whole-genome short-read sequences of 810 wild and domestic sheep representing 158 global populations and seven wild species, the use of T2T-sheep1.0 as the reference genome has improved population genetic analysis based on ~133.31 million SNPs and 1,265,266 SVs, including 2,664,979 novel SNPs and 196,471 novel SVs. T2T-sheep1.0 improves selective tests by detecting several novel genes and variants, including those associated with domestication (e.g., ABCC4) and selection for the wool fineness trait (e.g., FOXQ1) in tandemly duplicated regions.

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“…In cows, there are 12 IGHV, 16 IGHD, and 4 IGHJ functional segments (Deiss et al, 2019; Ma et al, 2016). Interestingly, a specific combination of V, D, and J segments (IGHV1‐7, IGHD8‐2, IGHJ2‐4) is utilized in the HCs of antibodies with ultra‐long CDRs (Deiss et al, 2019; Li et al, 2023; Stanfield et al, 2016). The LC germline genes can be assigned to one of two types—lambda (λ) or kappa (κ).…”

Section: Introductionmentioning

confidence: 99%

Specific features of a scaffolding antibody light chain

Trommer,

Lesniowski,

Buchner

et al. 2024

Protein Science

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The antigen‐binding sites in conventional antibodies are formed by hypervariable complementarity‐determining regions (CDRs) from both heavy chains (HCs) and light chains (LCs). A deviation from this paradigm is found in a subset of bovine antibodies that bind antigens via an ultra‐long CDR. The HCs bearing ultra‐long CDRs pair with a restricted set of highly conserved LCs that convey stability to the antibody. Despite the importance of these LCs, their specific features remained unknown. Here, we show that the conserved bovine LC found in antibodies with ultra‐long CDRs exhibits a distinct combination of favorable physicochemical properties such as good secretion from mammalian cells, strong dimerization, high stability, and resistance to aggregation. These physicochemical traits of the LCs arise from a combination of the specific sequences in the germline CDRs and a lambda LC framework. In addition to understanding the molecular architecture of antibodies with ultra‐long CDRs, our findings reveal fundamental insights into LC characteristics that can guide the design of antibodies with improved properties.

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De novo genome assembly depicts the immune genomic characteristics of cattle

Cited by 5 publications

References 66 publications

Telomere-to-telomere genome assembly of a male goat reveals novel variants associated with cashmere traits

Telomere-to-telomere genome assembly of a male goat reveals novel variants associated with cashmere traits

Telomere-to-telomere sheep genome assembly reveals new variants associated with wool fineness trait

Specific features of a scaffolding antibody light chain

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